Abstract: The unique hydrological variability of Poyang Lake strongly influences the distribution of vegetation growth and microbial metabolism, thereby affecting their carbon balance and greenhouse gas emissions. A two-dimensional hydrodynamic-DNDC (DeNitrification-DeComposition) model was constructed and validated with field and historical in-situ observations to study the dramatic seasonal water level fluctuations in Poyang Lake and the corresponding impact on the net ecosystem CO2 exchange in typical habitat zones (water body, submerged vegetation zone, and emergent aquatic plants-hygrophytes). The annual CO2 flux of the whole lake area was estimated based on Landsat remote sensing images. The results showed that: for the water body and the submerged plants zone, the total annual CO2 fluxes were basically the same for different typical years, whereas the annual CO2 fluxes of the emergent aquatic plants-hygrophytes were different for each typical year, with the highest CO2 emission in the dry year. The average annual CO2 fluxes of the three habitat zones were 566.4 (water body), 972.8 (submerged plant zone), and 3086.9 kg C/hm2/a (emergent aquatic plants-hygrophytes), the annual CO2 emission intensity of the emergent aquatic plants-hygrophytes was the highest. On the intra-annual distribution, the water body and submerged plants zone presented as stable carbon sources in all four hydrological periods of dry-rising-wet-falling, while the emergent aquatic plants-hygrophytes absorbed a large amount of CO2 in the rising and falling periods. The annual CO2 flux of Poyang Lake was 1.66±0.44 g CO2  ·m-2·d-1, which showed a carbon source. In addition, as the excessively high water level in wet years would shorten the plant growth time and lead to the evolution of vegetation in the direction away from the wetland, the CO2 emission from the wetland of Poyang Lake might be reduced for the condition of following average hydrological years with reduced water levels. The results of this paper clarified the key role of inter-annual and intra-annual water level changes on wetland CO2 emissions, which deepened the understanding of vegetation-mediated mechanisms in the carbon cycle process, and provided references for wetland management.